X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/c5795cc6f73d5affc55a332fcddc37fa56636f9a..95e5ccacf6c1193b313fa90a6d39baafa2ba67d8:/sdk/cwl/arvados_cwl/pathmapper.py diff --git a/sdk/cwl/arvados_cwl/pathmapper.py b/sdk/cwl/arvados_cwl/pathmapper.py index 998890a31c..d083b78f5a 100644 --- a/sdk/cwl/arvados_cwl/pathmapper.py +++ b/sdk/cwl/arvados_cwl/pathmapper.py @@ -8,14 +8,18 @@ import uuid import os import urllib +from arvados_cwl.util import get_current_container, get_intermediate_collection_info import arvados.commands.run import arvados.collection from schema_salad.sourceline import SourceLine +from arvados.errors import ApiError from cwltool.pathmapper import PathMapper, MapperEnt, abspath, adjustFileObjs, adjustDirObjs from cwltool.workflow import WorkflowException +from .http import http_to_keep + logger = logging.getLogger('arvados.cwl-runner') def trim_listing(obj): @@ -40,7 +44,7 @@ class ArvPathMapper(PathMapper): pdh_dirpath = re.compile(r'^keep:[0-9a-f]{32}\+\d+(/.*)?$') def __init__(self, arvrunner, referenced_files, input_basedir, - collection_pattern, file_pattern, name=None, single_collection=False, **kwargs): + collection_pattern, file_pattern, name=None, single_collection=False): self.arvrunner = arvrunner self.input_basedir = input_basedir self.collection_pattern = collection_pattern @@ -81,6 +85,10 @@ class ArvPathMapper(PathMapper): raise WorkflowException("File literal '%s' is missing `contents`" % src) if srcobj["class"] == "Directory" and "listing" not in srcobj: raise WorkflowException("Directory literal '%s' is missing `listing`" % src) + elif src.startswith("http:") or src.startswith("https:"): + keepref = http_to_keep(self.arvrunner.api, self.arvrunner.project_uuid, src) + logger.info("%s is %s", src, keepref) + self._pathmap[src] = MapperEnt(keepref, keepref, srcobj["class"], True) else: self._pathmap[src] = MapperEnt(src, src, srcobj["class"], True) @@ -107,6 +115,7 @@ class ArvPathMapper(PathMapper): elif obj["location"].startswith("_:") and "contents" in obj: with c.open(path + "/" + obj["basename"], "w") as f: f.write(obj["contents"].encode("utf-8")) + remap.append((obj["location"], path + "/" + obj["basename"])) else: raise SourceLine(obj, "location", WorkflowException).makeError("Don't know what to do with '%s'" % obj["location"]) @@ -120,19 +129,6 @@ class ArvPathMapper(PathMapper): keep_client=self.arvrunner.keep_client, num_retries=self.arvrunner.num_retries) - already_uploaded = self.arvrunner.get_uploaded() - copied_files = set() - for k in referenced_files: - loc = k["location"] - if loc in already_uploaded: - v = already_uploaded[loc] - self._pathmap[loc] = MapperEnt(v.resolved, self.collection_pattern % urllib.unquote(v.resolved[5:]), v.type, True) - if self.single_collection: - basename = k["basename"] - if basename not in collection: - self.addentry({"location": loc, "class": v.type, "basename": basename}, collection, ".", []) - copied_files.add((loc, basename, v.type)) - for srcobj in referenced_files: self.visit(srcobj, uploadfiles) @@ -143,16 +139,12 @@ class ArvPathMapper(PathMapper): fnPattern="keep:%s/%s", name=self.name, project=self.arvrunner.project_uuid, - collection=collection) + collection=collection, + packed=False) for src, ab, st in uploadfiles: self._pathmap[src] = MapperEnt(urllib.quote(st.fn, "/:+@"), self.collection_pattern % st.fn[5:], "Directory" if os.path.isdir(ab) else "File", True) - self.arvrunner.add_uploaded(src, self._pathmap[src]) - - for loc, basename, cls in copied_files: - fn = "keep:%s/%s" % (collection.portable_data_hash(), basename) - self._pathmap[loc] = MapperEnt(urllib.quote(fn, "/:+@"), self.collection_pattern % fn[5:], cls, True) for srcobj in referenced_files: remap = [] @@ -163,9 +155,14 @@ class ArvPathMapper(PathMapper): for l in srcobj.get("listing", []): self.addentry(l, c, ".", remap) - check = self.arvrunner.api.collections().list(filters=[["portable_data_hash", "=", c.portable_data_hash()]], limit=1).execute(num_retries=self.arvrunner.num_retries) - if not check["items"]: - c.save_new(owner_uuid=self.arvrunner.project_uuid) + container = get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger) + info = get_intermediate_collection_info(None, container, self.arvrunner.intermediate_output_ttl) + + c.save_new(name=info["name"], + owner_uuid=self.arvrunner.project_uuid, + ensure_unique_name=True, + trash_at=info["trash_at"], + properties=info["properties"]) ab = self.collection_pattern % c.portable_data_hash() self._pathmap[srcobj["location"]] = MapperEnt("keep:"+c.portable_data_hash(), ab, "Directory", True) @@ -177,9 +174,14 @@ class ArvPathMapper(PathMapper): num_retries=self.arvrunner.num_retries ) self.addentry(srcobj, c, ".", remap) - check = self.arvrunner.api.collections().list(filters=[["portable_data_hash", "=", c.portable_data_hash()]], limit=1).execute(num_retries=self.arvrunner.num_retries) - if not check["items"]: - c.save_new(owner_uuid=self.arvrunner.project_uuid) + container = get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger) + info = get_intermediate_collection_info(None, container, self.arvrunner.intermediate_output_ttl) + + c.save_new(name=info["name"], + owner_uuid=self.arvrunner.project_uuid, + ensure_unique_name=True, + trash_at=info["trash_at"], + properties=info["properties"]) ab = self.file_pattern % (c.portable_data_hash(), srcobj["basename"]) self._pathmap[srcobj["location"]] = MapperEnt("keep:%s/%s" % (c.portable_data_hash(), srcobj["basename"]), @@ -212,6 +214,7 @@ class ArvPathMapper(PathMapper): else: return None + class StagingPathMapper(PathMapper): _follow_dirs = True